ionize - Place ions

Introduction

Ionize is a threaded program for placing
counterions near a biological molecule in preparation for molecular
dynamics simulations. In this case, placement is performed by
calculating the coulombic potential due to the molecule in the nearby
volume, and placing ions at points of minimal energy. After each ion
is placed, the potential is updated, so that subsequent ions will
be placed in response to this. Unlike some ion placement tools,
ionize should be used *prior* to solvation so that the potential
from unequilibrated water does not interfere with it (the addition
of water would also make the energy calculations even more time
consuming). Ionize is designed to be used on multiple processors;
it uses a pthreads parallel implementation to run on shared memory
machines (any traditional multiprocessor machine, or shared memory
clusters such as an SGI Altix). After ionize is finished, you should
solvate your system normally.